Read the Docs build information
Build id: 146410
Project: cyverse-learning-materials-home
Version: latest
Commit: f0e245f1fe569de11311540e03fae0c9be7ef27c
Date: 2018-10-01T19:38:08.255107Z
State: finished
Success: True


[rtd-command-info] start-time: 2018-10-02T00:38:08.742665Z, end-time: 2018-10-02T00:38:08.750938Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/CyVerse-learning-materials/learning-materials-home.git


[rtd-command-info] start-time: 2018-10-02T00:38:08.812119Z, end-time: 2018-10-02T00:38:09.072699Z, duration: 0, exit-code: 0
git fetch --tags --prune
From https://github.com/CyVerse-learning-materials/learning-materials-home
   18ae32e..f0e245f  master     -> origin/master

[rtd-command-info] start-time: 2018-10-02T00:38:09.141040Z, end-time: 2018-10-02T00:38:09.148660Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 18ae32e... update links and add contribution quickstart
HEAD is now at f0e245f... fix description grammar

[rtd-command-info] start-time: 2018-10-02T00:38:09.263633Z, end-time: 2018-10-02T00:38:09.277695Z, duration: 0, exit-code: 0
git clean -d -f -f
Removing _build/
Removing misc/__init__.pyc
Removing misc/cyverse_sphinx_conf.pyc

[rtd-command-info] start-time: 2018-10-02T00:38:09.369383Z, end-time: 2018-10-02T00:38:09.375879Z, duration: 0, exit-code: 0
git branch -r
origin/HEAD -> origin/master
  origin/master

[rtd-command-info] start-time: 2018-10-02T00:38:10.079867Z, end-time: 2018-10-02T00:38:11.776900Z, duration: 1, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python2.7
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/bin/python2.7)
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2018-10-02T00:38:11.837424Z, end-time: 2018-10-02T00:38:14.050020Z, duration: 2, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Requirement already up-to-date: Pygments==2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: setuptools<40 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: docutils==0.13.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: pillow==2.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: commonmark==0.5.4 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: recommonmark==0.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx<1.8 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages
Requirement already up-to-date: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: packaging in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: typing; python_version < "3.5" in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from sphinx<1.8)
Requirement already up-to-date: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: urllib3<1.24,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from requests>=2.0.0->sphinx<1.8)
Requirement already up-to-date: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from packaging->sphinx<1.8)
Requirement already up-to-date: pytz>=0a in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from babel!=2.0,>=1.3->sphinx<1.8)
Requirement already up-to-date: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/envs/latest/lib/python2.7/site-packages (from Jinja2>=2.3->sphinx<1.8)
You are using pip version 9.0.1, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-10-02T00:38:15.154514Z, end-time: 2018-10-02T00:38:15.223061Z, duration: 0, exit-code: 0
cat conf.py
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# General information about the project.

import sys
import os
sys.path.insert(0, os.path.dirname(__file__))

from misc.cyverse_sphinx_conf import *  # noqa

project = 'CyVerse Learning Center Home'
copyright = '2017, CyVerse'
author = 'CyVerse'
version = '0.1b.0'
release = '0.1b.0'

epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    else:
        SUFFIX = source_suffix[0]
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = False
if 'html_theme' in globals():
    if html_theme in ['default']:
        # Allow people to bail with a hack of having an html_style
        if not 'html_style' in globals():
            import sphinx_rtd_theme
            html_theme = 'sphinx_rtd_theme'
            html_style = None
            html_theme_options = {}
            if 'html_theme_path' in globals():
                html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
            else:
                html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

            using_rtd_theme = True
else:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
    else:
        html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
    using_rtd_theme = True

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://media.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ],
    'downloads': [ 
    ("htmlzip", "//readthedocs.com/projects/cyverse-learning-materials-home/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
        ("cyverse-discovery-environment-guide", "https://learning.cyverse.org/projects/discovery-environment-guide/en/latest/"),
        ("cyverse-atmosphere-guide", "https://learning.cyverse.org/projects/atmosphere-guide/en/latest/"),
        ("cyverse-account-creation-quickstart", "https://learning.cyverse.org/projects/cyverse-account-creation-quickstart/en/latest/"),
        ("cyverse-importing-sradata-quickstart", "https://learning.cyverse.org/projects/cyverse-importing-sradata-quickstart/en/latest/"),
        ("cyverse-dnasubway-guide", "https://learning.cyverse.org/projects/dnasubway_guide/en/latest/"),
        ("cyverse-trimmomatic-quickstart", "https://learning.cyverse.org/projects/trimmomatic_quickstart/en/latest/"),
        ("cyverse-data-store-guide", "https://learning.cyverse.org/projects/data_store_guide/en/latest/"),
        ("cyverse-fastqc-quickstart", "https://learning.cyverse.org/projects/fastqc_quickstart/en/latest/"),
        ("cyverse-kallisto-tutorial", "https://learning.cyverse.org/projects/kallisto_tutorial/en/latest/"),
        ("cyverse-sra-submission-quickstart", "https://learning.cyverse.org/projects/sra_submission_quickstart/en/latest/"),
        ("cyverse-cyverse-tools-and-services-workshop", "https://learning.cyverse.org/projects/cyverse_tools_and_services_workshop/en/latest/"),
        ("cyverse-sciapps-guide", "https://learning.cyverse.org/projects/SciApps Guide/en/latest/"),
        ("cyverse-documentation-quickstart", "https://learning.cyverse.org/projects/Documentation-Quickstart/en/latest/"),
    ],
    'slug': 'cyverse-learning-materials-home',
    'name': u'learning-materials-home',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': 'https://learning.cyverse.org/en/latest/',
    'analytics_code': '',
    'single_version': False,
    'conf_py_path': '/./',
    'api_host': 'https://readthedocs.com',
    'github_user': 'CyVerse-learning-materials',
    'github_repo': 'learning-materials-home',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'f0e245f1',
}




if 'html_context' in globals():
    
    html_context.update(context)
    
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

[rtd-command-info] start-time: 2018-10-02T00:38:15.289028Z, end-time: 2018-10-02T00:38:16.495187Z, duration: 1, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 2 source files that are out of date
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] README
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/index.rst:207: WARNING: Duplicate substitution definition name: "CyVerse logo".
cyverse_rst_defined_substitutions.txt:110: WARNING: image file not readable: ./img/homeicon.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.md: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [ 50%] README
writing output... [100%] index

generating indices... genindex
writing additional pages... search
copying images... [ 50%] ./img/cyverse_platform_stack.png
copying images... [100%] ./img/cyverse_rgb.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying readthedocs static files... done
copying searchtools... done
copying extra files... done
dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 6 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2018-10-02T00:38:16.590143Z, end-time: 2018-10-02T00:38:17.672999Z, duration: 1, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... not yet created
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 2 added, 0 changed, 0 removed
reading sources... [ 50%] README
reading sources... [100%] index

/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/index.rst:207: WARNING: Duplicate substitution definition name: "CyVerse logo".
cyverse_rst_defined_substitutions.txt:110: WARNING: image file not readable: ./img/homeicon.png
cyverse_rst_defined_substitutions.txt:114: WARNING: image file not readable: ./img/intercom.png
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/README.md: WARNING: document isn't included in any toctree
done
preparing documents... done
assembling single document... 
writing... done
writing additional files...
copying images... [ 50%] ./img/cyverse_platform_stack.png
copying images... [100%] ./img/cyverse_rgb.png

copying static files... WARNING: html_static_path entry u'/home/docs/checkouts/readthedocs.org/user_builds/cyverse-learning-materials-home/checkouts/latest/_static' does not exist
WARNING: html_static_path entry '/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_static' does not exist
done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded, 6 warnings.

The HTML page is in _build/localmedia.